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- PDB-7zeq: Apo crystal structure of beta-xylosidase from Thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 7zeq
TitleApo crystal structure of beta-xylosidase from Thermotoga maritima
ComponentsBeta-xylosidase
KeywordsHYDROLASE / Apo Glycosyl hydrolase
Function / homology
Function and homology information


xylan 1,4-beta-xylosidase activity / beta-glucosidase / carbohydrate metabolic process
Similarity search - Function
Fibronectin type III-like domain / Fibronectin type III-like domain / Fibronectin type III-like domain / Glycoside hydrolase, family 3, active site / Glycosyl hydrolases family 3 active site. / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily ...Fibronectin type III-like domain / Fibronectin type III-like domain / Fibronectin type III-like domain / Glycoside hydrolase, family 3, active site / Glycosyl hydrolases family 3 active site. / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsGloster, T.M. / Foltanyi, F.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To be published
Title: Structural and further functional characterisation of a glycoside hydrolase family 3 beta-xylosidase from Thermotoga maritima
Authors: Gloster, T.M. / Foltanyi, F. / Hobbs, E.M. / Pritchard, L.
History
DepositionMar 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Beta-xylosidase
Y: Beta-xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,6884
Polymers179,4522
Non-polymers2362
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-39 kcal/mol
Surface area47520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.080, 98.590, 100.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11X
21Y

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 1 - 780 / Label seq-ID: 1 - 780

Dom-IDAuth asym-IDLabel asym-ID
1XA
2YB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Beta-xylosidase / TmGH3


Mass: 89725.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria)
Strain: ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8
Gene: Tmari_0073 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: R4NX63, xylan 1,4-beta-xylosidase
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 3% polyethylene glycol 8000, 48% 2-methyl-2,4-pentanediol, 0.1 M sodium cacodylate pH 5.9

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Data collection

DiffractionMean temperature: 175 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.89→55.402 Å / Num. obs: 143109 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 1 / Net I/σ(I): 49.3
Reflection shellResolution: 1.89→1.92 Å / Num. unique obs: 6970 / CC1/2: 0.39

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JP0, 5Z9S, 5YOT, 3U4A, 5XXL

5jp0

5z9s

5yot

3u4a

5xxl


Resolution: 1.89→55.402 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.205 / WRfactor Rwork: 0.173 / SU B: 4.509 / SU ML: 0.121 / Average fsc free: 0.8348 / Average fsc work: 0.8505 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.129 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2262 7250 5.069 %
Rwork0.1935 135788 -
all0.195 --
obs-143038 99.89 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 36.454 Å2
Baniso -1Baniso -2Baniso -3
1--2.677 Å2-0 Å20 Å2
2--2.796 Å2-0 Å2
3----0.119 Å2
Refinement stepCycle: LAST / Resolution: 1.89→55.402 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11719 0 16 182 11917
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01212003
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.63616233
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.86551517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.41321.927602
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.431152126
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0931586
X-RAY DIFFRACTIONr_chiral_restr0.0970.21538
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028990
X-RAY DIFFRACTIONr_nbd_refined0.2060.25049
X-RAY DIFFRACTIONr_nbtor_refined0.3140.28262
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.2441
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1660.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1460.29
X-RAY DIFFRACTIONr_mcbond_it2.7523.476068
X-RAY DIFFRACTIONr_mcangle_it3.4015.1837585
X-RAY DIFFRACTIONr_scbond_it4.3143.8395935
X-RAY DIFFRACTIONr_scangle_it5.9975.5648648
X-RAY DIFFRACTIONr_lrange_it6.46447.20717357
X-RAY DIFFRACTIONr_ncsr_local_group_10.060.0524774
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11XX-RAY DIFFRACTIONLocal ncs0.060480.0501
12YX-RAY DIFFRACTIONLocal ncs0.060480.0501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.89-1.9390.3965740.36497900.366104910.4470.45798.78940.354
1.939-1.9920.3475360.33196380.331101830.5420.55699.91160.315
1.992-2.050.2955390.28494150.28499560.7270.73999.97990.262
2.05-2.1130.2844810.25791570.25896400.8220.82199.97920.231
2.113-2.1820.284850.23388610.23593470.8560.87499.98930.205
2.182-2.2580.2554550.21686370.21890920.8890.9021000.187
2.258-2.3440.2444360.2183170.21287540.9040.91499.98860.179
2.344-2.4390.2443980.20180210.20384210.9130.92899.97620.17
2.439-2.5470.2644000.20377090.20681090.910.9281000.17
2.547-2.6710.2513860.20673940.20877800.9240.9291000.173
2.671-2.8150.2593930.19870120.20174050.9190.9381000.168
2.815-2.9860.2313620.19866230.269850.930.9381000.171
2.986-3.1910.2333050.19962610.20165670.9250.93599.98480.177
3.191-3.4460.2232640.18559080.18761730.9390.94999.98380.171
3.446-3.7730.1862660.16454040.16556700.9580.9651000.157
3.773-4.2160.192570.15749130.15851700.9640.9681000.155
4.216-4.8640.1692580.13643440.13846020.9730.9771000.141
4.864-5.9460.1771840.16137250.16239090.9650.971000.169
5.946-8.360.2061740.18829200.18930940.9610.9621000.201
8.36-55.4020.19970.17317390.17418400.9720.96899.78260.196

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